Take a look at the comment at http://drupal.org/node/530780#comment-2513534 which has the latest commands related to themes (actually, as of 3.0, but they seem to work with Drush 4.x as well).
- Disable theme:
drush -l http://example.com/ pm-disable theme_name - Enable theme:
drush -l http://example.com/ pm-enable theme_name - Change theme:
drush -l http://example.com/ vset theme_default theme_name - Change admin theme:
drush -l http://example.com/ vset admin_theme theme_name